<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<br>
Hi Nikolas,<br>
<br>
The reference base is taken from the input data, so if you enter: <br>
<div class="moz-cite-prefix"><br>
X 38147029 . C T . . .<br>
<br>
'C' is taken as the reference.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
On 07/05/2016 10:55, Nikolas Pontikos wrote:<br>
</div>
<blockquote
cite="mid:20160507095622.11E02132CD1_72DBBC6B@hx-mx2.ebi.ac.uk"
type="cite">
<div dir="ltr">
<div>The build 37 reference says that the ref allele is T but
VEP seems to think the ref allele is C.</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://grch37.ensembl.org/Homo_sapiens/Location/View?r=X%3A38147029-38147029">http://grch37.ensembl.org/Homo_sapiens/Location/View?r=X%3A38147029-38147029</a><br>
</div>
<div><br>
</div>
<div><a moz-do-not-send="true"
href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=EsPIGUsotU5cCbBz-1715935">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=EsPIGUsotU5cCbBz-1715935</a><br>
</div>
<div><br>
</div>
What's going on?</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>